02/03/2014

Research Scientist Spills the Beans

Ashley Egan joined the staff of the Department of Botany as Research Botanist and Assistant Curator of Legumes in August 2013.

Imagine starting a new job by going away on a three-month field excursion to the remote forests of China, Japan, and Thailand after only two weeks on the job, before having a chance to settle into your new office and unpack your boxes. Continue imagining that while you are away on your Asian expedition, you find out that your employer, the U.S. federal government, has shut down for 16 days, forcing you into “furlough in place” status (non-duty and non-pay). Such is the life of Ashley N. Egan, the Department of Botany’s new Research Botanist and Assistant Curator of Legumes.

Egan grew up in Idaho, spending her summers on the outskirts of Yellowstone National Park where she cultivated her love for nature. Her undergraduate studies were at Utah State University where she initially declared a major in Biological Engineering, and then switched to Biology and focused on population genetics. As an undergraduate, she volunteered in Paul G. Wolf’s laboratory, under the assistance of a Howard Hughes Medical Institute Undergraduate Research Fellowship. She studied the genetic differentiation between populations of Erythronium grandiflorum (Liliaceae). Egan’s honor’s thesis focused on the resolution of inter-simple sequence repeat (ISSR) markers in Ipomopsis aggregata and I. tenuituba (Polemoniaceae).

After graduating in 1998 with a B.S. in Biology, she stayed in Utah working as a laboratory technician under Lynn Bohs at the University of Utah where her work focused on the Solanaceae family. Egan soon shifted her attention from population genetics to phylogenetics and systematics.

In 2001 she began her graduate years at Brigham Young University, initially working on a doctoral thesis in cancer research. Her preliminary studies utilized phylogenetics as a means of bioprospecting, looking at the chemopreventive ability and phenolic content of the mint family, Lamiaceae. Unsatisfied with the direction of her thesis, Egan switched to Keith Crandall’s invertebrate biology laboratory, with the understanding that Egan would continue on with plant research.

Crandall suggested that Egan choose a plant system close to home, so Egan focused on the rare and endangered plant species of Utah. She settled on Pediomelum (Leguminosae), a genus with around 27 species across the United States and 70 percent listed as endangered or threatened. She explored the population history and conservation genetics of Pediomelum pariense, a rare species endemic to two counties in southern Utah. She asked questions about the relationship between the substrate in which P. pariense grows and its endemism in Utah. Her project then morphed into a species diversification study of tribe Psoraleeae, to which Pediomelum and four other genera endemic to the United States belong. Egan defended her dissertation, “Phylogenetics of North American Psoraleeae (Leguminosae): Rates and Dates in a Recent, Rapid Radiation,” in December 2006.

While conducting her doctoral research, Egan was in contact with Jeff Doyle at Cornell University. Egan and Doyle were exchanging outgroup material of Psoraleeae and soybean (Glycine max). In 2007, Egan became a postdoctoral research associate in Doyle’s lab, studying the phylogenetic systematics of subtribe Glycininae (Leguminosae). Egan’s research has determined that tribe Psoraleeae is nested within subtribe Glycininae, and is a potential progenitor genome of the polyploid soybean.

During her postdoctoral research, Egan began collaborating with several scientists studying soybean genome evolution. She was among a large group of co-authors who published several papers on genome evolution and polypoidy in soybean. As part of their research, they sequenced an approximately 1 million-base pair region in soybean and compared this region with its homoeologous region duplicated 10 to 14 million years ago. Their research produced several papers that focused on the evolution of disease resistance genes (Plant Physiology 148: 1740-1759; 2008), a large accumulation of retroelements (Plant Physiology 148: 1760-1771), and a comparison of retention or loss of disease resistance genes between the 20 million-year diverged soybean and Phaseolus vulgaris, the common bean (Plant Physiology 159: 336-354).

Egan and Doyle wrote a methodological discourse regarding the origins of polyploidy events (New Phytologist 186: 73-85; 2010). The paper argued that most studies that measure the date of polyploidy are actually measuring the date of divergence of progenitor genomes. They conclude that, “estimating the date of origin of a polyploid is difficult, and in some circumstances impossible.”

As a phylogeneticist, population geneticist, and comparative genomicist, Egan has an amazing toolkit that allows her to understand the processes and patterns that have formed biodiversity during the course of evolutionary change. With those skills she participated in another study during her post-doctoral years at Cornell that focused outside the plant world. The research examined adaptive horizontal transfer of a bacterial gene to an invasive insect species (Proc. Natl. Acad. Sci. 109: 4197-4202; 2012). Egan and her co-authors identified a gene from the coffee berry borer beetle, Hypothenemus hampei, which shows clear evidence of horizontal gene transfer from bacteria, an evolutionary change which seems to have enabled H. hampei to become a devastating pest of coffee.

In 2010, Egan was hired as an Assistant Professor of Biology during a Bioinformatics and Comparative Genomics search at East Carolina University (ECU). She continued her legume research, taking her work more towards systematics at the genus, subtribe, and tribe levels. As part of the Legume Phylogeny Working Group, she co-authored a paper that outlines the progress of legume phylogeny and classification and reviews taxonomic approaches from bioinformatics to next-generation sequencing (Taxon 62(2): 217-248; 2013). Egan also joined 29 co-authors to make a case for a Global Legume Diversity Assessment (GLDA), employing taxonomic, ecological, genetic, and phylogenetic approaches aimed at “clarifying uncertainties in and improving the understanding of biodiversity loss” (Taxon 62(2): 249-266; 2013).

While at ECU, Egan landed her first major grant from the National Science Foundation to study the evolutionary history, phylogenetics and population genetics of Kudzu (Pueraria montana var. lobata), a major invasive species introduced to the U.S. from Asia. With graduate student Matthew Hansen, she is examining how genetic variation differs between native and invasive populations of Kudzu and how many times Kudzu had been introduced to the U.S. Egan is also focusing on the taxonomy of Pueraria and Phaseoleae, a tribe of over 2,000 species worldwide. Since Egan returned from Asia, and in addition to unpacking her office boxes, she is busy with the nearly 850 plant specimens collected during her field work which was largely focused on the genus Pueraria and other phaseoloid legume collections.

At the Smithsonian, Egan will continue studying the adaptation, speciation, endemism, biogeography, polyploidy, and conservation genetics of the Psoraleeae and Phaseoleae tribes. In her research on Glycininae, she plans to continue in her search for the progenitor genome(s) of soybean, including key players Psoraleeae and kudzu (Pueraria montana var. lobata). She is planning to take her research towards phylogenomics by using targeted enrichment via next generation sequencing to understand the evolutionary history of phaseoloid legumes.

The legume collection at the U.S. National Herbarium will play a large part in Egan’s current and future research. The legume collection ranks among the largest in the herbarium, after the Asteraceae and Poaceae collections. Over 86,000 legume specimens have been inventoried, including the entire Caesalpinioideae collection. The Type Herbarium includes 7,454 legume specimens. Egan hopes to enhance the legume collection by addressing the significant backlog of unmounted and unidentified specimens in addition to reorganizing the collection phylogenetically. She hopes to increase the collection with a greater representation from across the world through her own collecting activities and through exchanges with other herbaria.

Egan follows in the footsteps on other notable legume specialists that have worked at or have been affiliated with the Smithsonian Institution. Charles Vancouver Piper (1867-1926) received a Master’s degree in botany from Harvard in 1900, and taught there until 1903. He was then hired by the U.S. Department of Agriculture and became curator of grasses until 1905, when Albert Spear Hitchcock (1865-1935) assumed the position. He was put in charge of the office of Forage Crop Investigations from 1905 until his death in 1926. He is best known for his monumental monograph, The Soybean, with William J. Morse. With Morse, Piper was largely responsible for the introduction of the soybean into the U.S., and subsequently into the agriculture of other Western countries. His principal taxonomic revisionary works are with many genera in the legume tribe Phaseoleae. Aside from Piper’s work with legumes, he published substantial floristic works of northwestern U.S.

Velva E. Rudd (1910-1999), a specialist in tropical Leguminosae, received her Ph.D. in Botany from George Washington University in 1953. She joined the Department of Botany first as a technician under Kitty Parker, and then as an Assistant Curator in 1948. She served as Curator from 1959 until her retirement in 1973. Rudd wrote more than 70 papers on legume taxonomy, including a six-part monograph in Contributions from the United States National Herbarium (1955-1968) focusing on seven genera (Aeschynomene, Ateleia, Chaetocalyx, Cyathostegia, Dussia, Nissolia, and Ormosia). Her field work took her to Mexico, Costa Rica, Brazil, Venezuela, Ceylon (now Sri Lanka), and other places. The Mexican legume genus Ruddia is named for her, as well as several legume species. Before her death in 1999, she submitted several generic treatments for the upcoming legume volume in Flora of North America.

In 1957 Richard S. Cowan (1921-1997) joined the Department of Botany as an Associate Curator. Cowan was a specialist in the taxonomy of Neotropical caesalpinioids and in the flora of northern South America. He became the Assistant Director of the National Museum of Natural History in 1962 and Director from 1965-1972. After 1972, Cowan returned to the Department of Botany as a Senior Botanist. He retired from the Smithsonian in 1985. He led notable expeditions and initiated floral surveys of Dominica and British Guiana. Noteworthy research included taxonomic studies on Swartzia and Eperua. Cowan co-organized the first International Legume Conference at the Royal Botanical Gardens Kew in 1978, and co-founded the legume systematics newsletter, The Bean Bag, which he edited from number 1 (1975) to number 12 (1980). One of his most significant scientific achievements was his work with Frans A. Stafleu (1921-1997) on Taxonomic Literature 2, a guide to the literature of systematic botany published between 1753 and 1940.

Other notable legume specialists in the Washington, DC area have been affiliated with the Department of Botany and have made significant long-term contributions to the collections. Charles Robert "Bob" Gunn, USDA and curator of the National Seed Herbarium, published revisionary work in the genus Vicia and extensive taxonomic works in legume seeds. Joseph H. Kirkbride, Jr. assumed curatorship upon Gunn's retirement. He is the primary author of the monumental two-volume work Fruits and Seeds of Genera in the Subfamily Faboideae (Fabaceae) (2003) and has published systematic works in Lotus and Swartzia relatives. Patrick S. Herendeen (Chicago Botanic Garden) worked extensively with the Caesalpinioideae collections.

James A. Lackey worked extensively with the Phaseoleae collections during a postdoctoral fellowship 1977-1978, resulting in several revisionary and floristic treatments and the Phaseoleae generic classification overview for the first International Legume Conference. He assumed editorship of The Bean Bag from Cowan in 1980. Upon retirement from USDA, he has published taxonomic, agricultural, and anatomical work in overall papilionoid legumes, Phaseoleae, Swartzia and related genera.